Merge pull request #8 from csdms/mcflugen/update-repository

Update repository

.github/workflows/test.yml

@@ -0,0 +1,54 @@
+name: Test
+
+on: [push, pull_request]
+
+jobs:
+  build-and-test:
+    # We want to run on external PRs, but not on our own internal PRs as they'll be run
+    # by the push to the branch. Without this if check, checks are duplicated since
+    # internal PRs match both the push and pull_request events.
+    if:
+      github.event_name == 'push' || github.event.pull_request.head.repo.full_name !=
+      github.repository
+
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Test
+        run: |
+          pip install nox
+          nox --non-interactive --error-on-missing-interpreter -s test test-notebooks
+
+      - name: Coveralls
+        if: matrix.os == 'ubuntu-latest'
+        uses: AndreMiras/coveralls-python-action@develop
+        with:
+          parallel: true
+          flag-name: py${{ matrix.python-version }}-${{ matrix.os }}
+
+          debug: true
+
+  coveralls_finish:
+    needs: build-and-test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Coveralls Finished
+        uses: AndreMiras/coveralls-python-action@develop
+        with:
+          parallel-finished: true
+          debug: true

.gitignore

@@ -1,107 +1,8 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
+*.egg-info/
+*.ipynb_checkpoints/
 *.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
+.coverage
+.nox/
+__pycache__/
 build/
-develop-eggs/
 dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-
-# pycharm idea folder
-.idea/

.pre-commit-config.yaml

@@ -0,0 +1,92 @@
+repos:
+- repo: https://github.com/psf/black
+  rev: 23.12.1
+  hooks:
+  - id: black
+    name: black
+    description: "Black: The uncompromising Python code formatter"
+    entry: black
+    language: python
+    language_version: python3
+    minimum_pre_commit_version: 2.9.2
+    require_serial: true
+    types_or: [python, pyi]
+  - id: black-jupyter
+    name: black-jupyter
+    description:
+      "Black: The uncompromising Python code formatter (with Jupyter Notebook support)"
+    entry: black
+    language: python
+    minimum_pre_commit_version: 2.9.2
+    require_serial: true
+    types_or: [python, pyi, jupyter]
+    additional_dependencies: [".[jupyter]"]
+
+- repo: https://github.com/adamchainz/blacken-docs
+  rev: 1.16.0
+  hooks:
+  - id: blacken-docs
+
+- repo: https://github.com/keewis/blackdoc
+  rev: "v0.3.9"
+  hooks:
+  - id: blackdoc
+
+- repo: https://github.com/pycqa/flake8
+  rev: 7.0.0
+  hooks:
+  - id: flake8
+    additional_dependencies:
+    - flake8-bugbear
+    - flake8-comprehensions
+    - flake8-simplify
+
+- repo: https://github.com/nbQA-dev/nbQA
+  rev: 1.7.1
+  hooks:
+    - id: nbqa-pyupgrade
+      args: ["--py310-plus"]
+    - id: nbqa-isort
+    - id: nbqa-flake8
+      args: ["--extend-ignore=E402"]
+
+- repo: https://github.com/kynan/nbstripout
+  rev: 0.6.1
+  hooks:
+    - id: nbstripout
+      description: Strip output from jupyter notebooks
+      args: [--drop-empty-cells]
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.15.0
+  hooks:
+  - id: pyupgrade
+    args: [--py310-plus]
+
+- repo: https://github.com/asottile/reorder-python-imports
+  rev: v3.12.0
+  hooks:
+  - id: reorder-python-imports
+    args: [--py310-plus, --add-import, "from __future__ import annotations"]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+    - id: check-builtin-literals
+    - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-toml
+    - id: check-yaml
+    - id: debug-statements
+    - id: end-of-file-fixer
+    - id: forbid-new-submodules
+    - id: mixed-line-ending
+    - id: trailing-whitespace
+    - id: name-tests-test
+    - id: file-contents-sorter
+      files: |
+        (?x)^(
+          .*requirements(-\w+)?.(in|txt)|
+          requirements/.*\.txt|
+          .gitignore
+        )

.readthedocs.yaml

@@ -0,0 +1,17 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+sphinx:
+  builder: html
+  configuration: docs/source/conf.py
+  fail_on_warning: false
+
+python:
+  install:
+    - requirements: requirements_doc.txt
+    - method: pip
+      path: .

LICENSE.txt → LICENSE.md

@@ -1,6 +1,6 @@
-MIT License
+# The MIT License (MIT)
 
-Copyright (c) 2020 Tian Gan
+Copyright (c) `2020` `Tian Gan`
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal